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CHEK2
Final classification
VUS
CHEK2 c.953G>A · p.Arg318His
CHEK2

NM_007194.4:c.953G>A (p.Arg318His) is a missense variant in CHEK2 exon 9, located within the kinase domain. The variant has been observed at extremely low frequency in population databases (gnomAD v2.1: 13/282,864 alleles, AF=0.0046%; v4.1: 73/1,613,934 alleles, AF=0.0045%), consistent with PM2 at supporting level.

Gene
CHEK2
Transcript
NM_007194.4
HGVS · transcript:coding
NM_007194.4:c.953G>A
Consequence
N/A
GRCh38
chr22:28699893 C>T
GRCh37
chr22:29095881 C>T
Basis Hereditary Breast, Ovarian and Pancreatic Cancer Specification v1.0.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Hereditary Breast, Ovarian and Pancreatic Cancer Specification v1.0.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
CHEK2 c.953G>A

NM_007194.4:c.953G>A (p.Arg318His) is a missense variant in CHEK2 exon 9, located within the kinase domain. The variant has been observed at extremely low frequency in population databases (gnomAD v2.1: 13/282,864 alleles, AF=0.0046%; v4.1: 73/1,613,934 alleles, AF=0.0045%), consistent with PM2 at supporting level.1 Computational in silico tools uniformly predict a benign effect: REVEL score 0.061, BayesDel score -0.127872, and SpliceAI max delta 0.00, supporting BP4 at supporting level.2 Dong et al. (2003, PMID:12533788) identified this variant in 1 of 94 early-onset prostate cancer cases and 0 of 423 unaffected controls; it was not found in familial prostate cancer cases, and the single observation does not achieve statistical significance for PS4.3 ClinVar reports this variant as Uncertain Significance (15 clinical laboratories) and Likely Benign (1 laboratory). No expert panel has classified this variant.4 With PM2 (supporting pathogenic) and BP4 (supporting benign) applied, the evidence is balanced. The variant is classified as Variant of Uncertain Significance (VUS). Additional functional data (BS3/PS3) and case-control studies (PS4) are needed to resolve the classification.

PM2 + BP4 VUS
Gene diagram · NM_007194.4 · variants mapped to exon structure
CHEK2 NM_007194.4
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 4.52311e-05; MAF= 0.00452%, 73/1613934 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 0.000116733; MAF= 0.01167%, 7/59966 alleles, homozygotes = 0); grpmax FAF= 5.437e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 4.59585e-05; MAF= 0.00460%, 13/282864 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 0.000112867; MAF= 0.01129%, 4/35440 alleles, homozygotes = 0); grpmax FAF= 3.893e-05.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0045% · 73 / 1,613,934
      0 hom · FAF 0.0054%
      Admixed American
      7 / 59,966
      0.012%
      European (non-Finnish)
      63 / 1,180,000
      0.0053%
      East Asian
      1 / 44,886
      0.0022%
      African/African American
      1 / 74,898
      0.0013%
      South Asian
      1 / 91,076
      0.0011%
      + 5 not observed (Remaining individuals, European (Finnish), Amish, Middle Eastern, Ashkenazi Jewish)
      gnomAD v2.1
      0.0046% · 13 / 282,864
      0 hom · FAF 0.0039%
      Admixed American
      4 / 35,440
      0.011%
      European (non-Finnish)
      7 / 129,168
      0.0054%
      East Asian
      1 / 19,952
      0.005%
      South Asian
      1 / 30,614
      0.0033%
      + 4 not observed (African/African American, Ashkenazi Jewish, European (Finnish), Remaining individuals)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (15 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 133890)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.061. BayesDel score = -0.127872.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. CHEK2, an intracellular kinase involved in control of the cell cycle, is altered in various cancer types.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 PMIDs not cited in assessment
      12533788 ↗ Mutations in CHEK2 associated with prostate cancer risk. CLINVAR
      22419737 ↗ Response to DNA damage of CHEK2 missense mutations in familial breast cancer. CLINVAR
      23555315 ↗ Genome-wide testing of putative functional exonic variants in relationship with breast and prostate cancer risk in a multiethnic population. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      26845104 ↗ Improving performance of multigene panels for genomic analysis of cancer predisposition. CLINVAR
      30303537 ↗ Familial breast cancer and DNA repair genes: Insights into known and novel susceptibility genes from the GENESIS study, and implications for multigene panel testing. CLINVAR
      34933735 ↗ Exonic sequencing and MLH3 gene expression analysis of breast cancer patients. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR